added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / rarefact.cpp

diff --git a/rarefact.cpp b/rarefact.cpp
index f5e7952688cdbb1dd182ca44df9c152ef46879d9..691d01708bab5b5bef4118ab38662819280b56de 100644 (file)
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -12,13 +12,18 @@
 
 /***********************************************************************/
 
-int Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
        try {
                RarefactionCurveData* rcd = new RarefactionCurveData();
                for(int i=0;i<displays.size();i++){
                        rcd->registerDisplay(displays[i]);
                }
-       
+               
+               //convert freq percentage to number
+               int increment = 1;
+               if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+               else { increment = percentFreq;  }      
+                       
                for(int iter=0;iter<nIters;iter++){
                
                        for(int i=0;i<displays.size();i++){
@@ -73,7 +78,7 @@ int Rarefact::getCurve(int increment = 1, int nIters = 1000){
 
 /***********************************************************************/
 
-int Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
 try {
                SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
                
@@ -87,6 +92,11 @@ try {
                //if jumble is false all iters will be the same
                if (globaldata->jumble == false)  {  nIters = 1;  }
                
+               //convert freq percentage to number
+               int increment = 1;
+               if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+               else { increment = percentFreq;  }
+               
                for(int iter=0;iter<nIters;iter++){
                
                        for(int i=0;i<displays.size();i++){